RNA interactions in the regulation of transcription

In this overview we describe interactions between RNA, DNA, and proteins that are involved in the regulation of the various functional cycles of E. coli transcription. The role of the RNA terminator hairpin in destabilizing the transcription elongation complex and controlling the efficiency of termination at various template positions near intrinsic terminators are discussed, as are the mechanisms whereby rho protein triggers RNA release at rho-dependent terminators. Mechanisms used by phage 1-coded antitermination factor N in "fine-tuning" termination efficiencies are also considered, as are the roles of kinetically different elongation complex conformations in controlling transcriptional fidelity. General principles of the control of transcription by such RNA-protein interaction mechanisms are discussed.